Rapid non-invasive prenatal Down syndrome detection using a DNA-molecule counter Abstract Down syndrome (DS) is the most common survivable genetic disorder affecting 1 in 691, or approximately 6,000 live births in the United States annually. Current non-invasive prenatal screening tests based on ultrasound and blood sample measurements are inaccurate, and confirmatory tests such as chorionic villus sampling and amniocentesis are invasive procedures that can cause miscarriage. Recently, a new non-invasive massively parallel sequencing test to detect trisomy 21 in the fetal DNA present in maternal plasma has become available. Although the approach produces a definitive diagnosis for aneuploidy without risk to the fetus, the test is expensive, and expectant parents usually have a long wait time of ten days or more. To improve the current method, our objective is to develop a faster and cheaper single molecule counting system to detect fetal aneuploidy from maternal plasma DNA. We recently demonstrated a novel approach to count single molecules of DNA. A collection of sequence barcodes is used to randomly label individual DNA molecules, and after amplification, the number of different barcodes can be easily detected and counted to reveal the number of copies of identical molecules originally present. Thus, we transform the difficult task of counting individual copies of identical molecules into a simple one of detecting the number of different barcodes present. In our published work, we used a microarray detector to count barcodes, and showed precise and accurate digital, absolute quantitation of chromosomal copies starting with very low, sub-nanograms of sample input. For this proposed pilot study, we will further define the barcoding and amplification reaction conditions, and construct a suitable microarray barcode counter to enable the detection of very small increases of additional copies of chromosome 21. The measurement accuracy and statistical confidence of our detection method will be thoroughly investigated to demonstrate feasibility for a subsequent commercial product development phase. Our company is composed of key leaders in the field including Stephen Fodor who was the first to invent and develop microarray technology, and Stephen Quake who was the first to demonstrate single molecule DNA sequencing and a non-invasive prenatal test for Down syndrome. Both founders will play critical roles in the development and commercialization of this novel technology. Additionally, we have established collaborations with Ronald Davis at the Stanford University Genome Technology Center, giving us access to instruments and expertise available at this world class research facility.